[Colin Carver]"The new feature in CS6 to be able to import vector images and make them into true 3D layers is pretty impressive, but for the life of me I can't figure out to apply certain effects to these layers. For example, how can I apply a directional blur to one of these ray-traced layers? If I do it the normal way, nothing happens. Is it because of the 3D properties? of the layer Will I have to render out the animation and then apply the blur to that?"

Ray tracing [link] is a technique for simulating how light (rays) bounces off of objects (geometry & materials) before hitting our eyes (camera). A ray tracing renderer starts at the camera and works backwards, tracing rays out of the camera, following the ones that intersect and bounce off of objects (over a specified number of reflections) to their origins in a light source. The light source and the properties of the materials its rays hit affect both affect the appearance of the image.

Effects like directional blur are 2D image manipulations. Because they calculate pixels, not geometry or light interactions, they don't make sense in the context of ray tracing.

These new 3D objects are based on the geometry of swept surfaces, which is a radical departure from the pixel-based text and shapes in the Classic 3D renderer. As such, masking, effects, and track mattes don't make sense when applied to geometry. The geometrical properties of text and shapes are preserved, so character styles like kerning, font size, and subscript are supported.

To combine pixel-based effects with ray-traced objects, you'll have to do as you've suggested -- treat the ray-traced comp as a 2D/2.5D source in a Classic 3D comp.